DIANA/LncBase v3

1. What sort of data is it? What sort of information does it offer us?

DIANA tools have been developed and focused on the expression analysis, annotation of the elements and targets that are involved in the regulatory mechanisms of microRNAs, and determining the effects of microRNAs in development of different disorders. DIANA tools include, but not limited to, microCLIP, miRGen v4, lncBase v3, and microT-CDS.

2. When and where was it published? Was it published?

Initially it was published in 2009. Tthe University of Thessaly (UTH), Hellenic Pasteur Institute (HPI), and the Information Management Systems Institute (IMSI) of ‘Athena’ Research Center.

3. Is this annotation set updated regularly or is it a static source?

Although it is not a static source, it is not updated regulary.

4. Where can I find this data?

(link to the download web address or ftp site or publica!on where it can be found) https://diana.e-ce.uth.gr/tools

5. How is the data formatted and released? Does it exist in some sort of standard file format?

There are various other resources that are integrated to predict, and compute different interactions at different levels. For each source, the standard format of the source is refered.

6. What identifiers are associated with these annotations?

Gene name (symbol), miRNA name, ensembl transcript_id

References

Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG. DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W273-6. doi: 10.1093/nar/gkp292. Epub 2009 Apr 30. PMID: 19406924; PMCID: PMC2703977.

Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG. DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W169-73. doi: 10.1093/nar/gkt393. Epub 2013 May 16. PMID: 23680784; PMCID: PMC3692048.

Karagkouni D, Paraskevopoulou MD, Tastsoglou S, Skoufos G, Karavangeli A, Pierros V, Zacharopoulou E, Hatzigeorgiou AG. DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts. Nucleic Acids Res. 2020 Jan 8;48(D1):D101-D110. doi: 10.1093/nar/gkz1036. PMID: 31732741; PMCID: PMC7145509.

Paraskevopoulou, M.D., Karagkouni, D., Vlachos, I.S. et al. microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions. Nat Commun 9, 3601 (2018). https://doi.org/10.1038/s41467-018-06046-y

Steipe, B. Modified: Isserlin, R. (2020-01-02) BCB420 - Computational System Biology. Retrieved 2023-01-20 from: BCB420 Winter 2023 course material